Primary microcephaly (MCPH) is a congenital, static, and non-progressive neurodevelopmental disorder associated with reduced head circumference (< 4 standard deviations). About 28 known genes are associated with the MCPH. The study was carried out to probe molecular basis and genetic variants involved with MCPH in an affected Pakistani family to better understand the etiology and prevalence of the disorder. The individuals of the ascertained Pakistani family presented primary microcephaly, along with intellectual disability, speech disorder, and motor delay. By ensuring ethical compliance and patient consent, blood samples were collected from affected individuals. DNA was extracted using the salting out method followed by whole-exome sequencing and Sanger sequencing to identify causative genetic variants or mutations. In silico studies were performed to predict the effect of mutations on the structure of target proteins. Two missense allelic variants (NM_024596.5: c.139G>C and NM_024596.5: c.211G>C) of MCPH1 gene were detected in a Pakistani family. In silico analysis was performed to evaluate the effect of the mutant protein. The mutation in genes affects the activities of proteins NM_024596: p. Val47Leu and NM_024596: p. Val71Leu respectively by disruption in protein structure. The mutations were predicted to have higher pathogenicity scores and have significantly influenced the prevalence of MCPH. We reported two novel genetic variants for the first time from the Pakistani population causing MCPH. Mutations in MCPH1 gene are one of the major causes of MCPH in the populations where consanguine marriages are common. The novel mutations identified in this study will help to understand the etiology of the disorder and the mechanisms of mutated proteins.

Keywords: primary microcephaly, MCPH1, exome mapping, mutation, proteins, in silico